


The Lonely Shepherd

by EdgeOfSanity



Category: Doctor Who, doctor who 2010
Genre: Amy having more second thoughts than showed, Angst, Drama, Fanfiction, Gen, Supernatural - Freeform
Language: English
Status: Completed
Published: 2015-09-02
Updated: 2015-09-02
Packaged: 2018-04-18 17:18:24
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,538
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4714112
Author URL: https://archiveofourown.org/users/EdgeOfSanity/pseuds/EdgeOfSanity
Summary: <blockquote class="userstuff">
              <p>Amy knows the Doctor will be back. He always comes back, even if to say ‘hello’. But there is something odd this time, something she knows has changed him but she can’t put her finger on it. This can only end up going terribly wrong or fantastically right. Nothing is ever mid-way with them. AU! Set almost right after Vincent and the Doctor up until The Power of Three, partly canon. Spark of Dark!Doctor here and there.</p>
            </blockquote>





	The Lonely Shepherd

**Author's Note:**

> Lately, I’ve wanted to write a Doctor/Any Companion supernatural fic. Since May to be honest, even a 1000 word drabble would’ve sufficed. But I guess it’s not meant to be, so Ha. Title is from Zamfir’s The Lonely Shepherd. Great instrumental right thur. Lyrics belong to Big Data’s Dangerous. R&R is lovely.
> 
> That’s all, really. Well, that and the Doctor’s kind of OOC and its mainly told from Amy’s POV. Things get a little craz-zay. But not too craz-zay. Now without further Adieu…
> 
> Enjoyxx

It started with the flower. It never starts with a flower and it's almost as if he's sorry for something. But here they are, blue (Amy decides to call this 'TARDIS blue') flowers shaped like pods setting peculiarly on her doorstep in a green vase one cloudy day she goes to check the mail, the note underneath calls it a Jade Vine and explained they can only be seen in the rain forest of the Philippines—while bats are its natural pollinators, making it appear to illuminate at night. They aren't your traditional Roses because he is not a romantic and far from traditional. These are spontaneous. They make a statement without being obvious. Kind of like the Doctor, you never really noticed him until he was right in front of you. Then you wondered how you ever missed someone like him in the first place. Or something like him.

_'Stop waiting and live.'_

He'd attached a card and she didn't grasp why he bothered. Amy knows she isn't wasting her life so much as living vicariously through a 'mad man' with a time machine. On second thought, maybe that sounded a little selfish to people who didn't know them, the 'outsiders' is what she was personally fond of calling them, but knew he secretly loved it just as she did.

It began with a trip to the Arctic Drilling Station, when a nano-virus had spread through the crew because of Cybermats trying to recover former Cybermen trapped beneath ice a millennia ago. Only once they had defeated the enemy and safely returned to the TARDIS did she notice the small bite marks on his wrist, which he quickly covered up.

"Nothing. Its nothing," Just 'scratches' or possibly a bug bite is what he would hesitantly admit later.

Except there were no bugs in the Arctic, at least not any that left a bite mark the size of a dime.

"Doctor..." She tilted her head, inquiring, though she knows it's a fragile and awkward venture. He's already created space between them, she thinks of it as his own personal 'Safe-Guard'. It's an unspoken rule that they're best friends, but they both can see the relationship still has a few nagging bumps and bruises.

"Amy." He says her name as if its an affirmation; she doesn't know why because he shouldn't need support in knowing that she will always be there for him. He looks up from the controls and she frowns as his finger makes its way to his mouth, unaware to anyone but Amy that this is a new habit. The conversation that has barely begun is over and he goes on to babble about Space Florida.

He doesn't realize his index finger is bleeding.

Amy considered what a bite like that would to a Time Lord. Probably nothing. Probably nerves, on her part.

Probably.

She didn't have much time to think it over when they met River Song again. Just a fun (quiet and certainly no running) trip to the oldest planet in the universe, he'd said, nothing too special except some ancient writing, and the little fact that its importance has never been discerned. The Doctor was astonished as a puppy to find that he and Amy were the only two to read it, but as usual, even the most insignificant things had the biggest chain reaction when traveling with him. She remembered taking River aside only once before entering the cave below the Stonehenge.

"Love, it'll never be easy. But you'll make it bearable. Trust me." A smile flittered over her lips that was somehow both dubious and complacent. It was one Amy could not bring herself to get used to and she felt this wouldn't be the last time she'd see it.

"I know, of course I know. But you don't understand. It's like pulling teeth with him sometimes. He gets completely wrapped up in whatever he's doing until he forgets to think and it's been happening a lot more lately. How did you know, anyway?"

"That's because he doesn't want to think, sweetie." She stuck out her tongue and Amy caught on, prompting them both to say 'Spoilers' in unison, also earning them an eyebrow raise from the Doctor that reached his hairline.

This happened a few months ago, maybe a week, she couldn't be sure to any further extent and whether it was because of the paradox or not, and she couldn't bring herself to care. She was just happy to remember Rory again and grateful he decided to wait two thousand years. She isn't sure she could do the same. They had both done enough waiting to last a lifetime, but none of that really mattered anymore because then she had finally married the most beautiful person she had ever met. Not that he knew it, she still wasn't sure what kind of effect that would have on their relationship if she told him. It was also one of the most important things she had ever done— so what if she didn't get to raise Melody as a normal child or see her off every day to school like most parents? Nothing in her life would ever be considered normal.

Then there was the Minotaur. She hated to blame the poor creature but couldn't help it, had they not gone to that hotel doubled as a prison, maybe he wouldn't have left them. In his defense, he did give them a house and a new car Rory had always wanted, though it wasn't enough to Amy. It was all or nothing and she's probably being selfish, she knows this, and yet is powerless to stop it.

It wasn't until that night the Doctor stopped to pick them up in the wee hours of the morning, to cater them off to save yet another planet no less, and rambling on about utter nonsense that she realized just how worse things would've gotten regardless of the Minotaur.

That doesn't mean she didn't get up the second time he visited after deciding to delete such a petty voice mail, which isn't nearly enough to satisfy him when it came to seeing his favorite people.

The TARDIS was unerringly how she remembered it, how could she expect any different? She guessed a part of her expected the ship to forget her and their travels together. Before Rory and the countless aliens across space, when she was wide-eyed and blissfully unaware of how many times one could be put in dangerous situations and come out unscathed—on the surface. She left Rory comfortably snoring when her bare feet made contact with the familiar chill of the floor; she hadn't bothered with slippers, as she liked it better this way. It reminded her of that first night...

"So, uh, how're you?"

There was an awkward pause. Amy frowned, since when were they considered awkward with each other? She brushed away the feeling and instead went to hug him, but he stiffened under her touch. She pulled away and looked at him worriedly, while he avoided her eyes. "What is it? Have I done something? You're the one who interrupted our beauty sleep, Poncho."

"No, it's just...no." He shuddered a bit; it felt as if someone had walked over his grave. Knowing his chaotic timeline, perhaps they did. "Are you and Rory well?" She nodded, still unsure as to why he'd chosen to visit at this hour. "Good! Brilliant. Sorry to pop in out of the blue, but you have to see the colossal view of the solar system on this planet! And the planet itself is shaped like a diamond! Well, actually it's more likely a crater and I didn't think to check for reservations at the Inn, though I'm sure—What? What's the look for?"

She blinked, somewhat taken aback.

"Doctor, I just asked if you were all right a minute ago. Didn't you hear me?"

"Right, yes," After a brief moment of rubbing his temples, he pressed a button that sent the TARDIS swaying to the right, and causing her to grab the railing for dear life, before steadying again. "Sorry, you did? Haven't been getting much sleep."

"I can see that," A smirk crept its way across her face; the dark circles forming under his eyes and the new signs of grey hair were hard to miss. "Did you miss us?"

"Of course I missed you two!"

"Then why don't you come 'round more often?"

He stilled. Pressing a few more buttons before finally facing her. "What makes you think I haven't?"

"What, you've been spying on us? Why didn't you just phone ahead? You left enough messages."

His jaw clenched. Couldn't she see the affect she had on him?

"Not spying, Amy. Never spying. Only...a short trip here or there. Speaking of," He dashed past her and threw open the TARDIS doors, revealing a rather foggy, dessert landscape. "Welcome to Cronous Craterous, Pond. Sector 9 to be exact. One of the oldest craters in space, and the most unknown amongst humans—who first mistaken it for the moon." He laughed a little as they stepped out into the gritty and dry plain. She frowned after he bounded off in the direction of what looked to be a small city, replaying how his laugh had sounded almost threatening in her mind.

She rolled her eyes and dismissed the idea; she was on a new planet (crater—whatever) for God sake! She couldn't allow some silly speculation ruin the whole trip and besides, she hadn't traveled with him in awhile. Maybe he was tired. In her defense however, she voiced that he was never more right in his life; the stars were quite a breathtaking sight.

Still...she couldn't shake the feeling during the short time it took for them to explore, eat, and run from some very unhappy locals when they saw their prized and highly protected Staff of Wisdom being 'vandalized'. Said Staff held a diamond the size of a tennis ball within a carved three-clawed hand. Which meant the Doctor obviously needed a closer look by pulling it off the low shelf and using his sonic, thus began setting off the alarm, the accusations of stealing, and running, mostly running. Since half of Amy's recollection of this planet is a blur. All of this happened in such order, like clockwork some might say, it could be considered funny.

Had it not been for the laugh that cast a veil of uneasiness over her the entire run back, and not from the locals who carried spears that could cut clean through flesh like a newly sharpened scalpel.

"...I should probably drop you off back home." Is the first thing the Doctor said, settling the TARDIS into the vortex and watching Amy sitting on the captain's seat attempting to catch her breath. "I'm sure Rory misses you, and the house must be total chaos. This trip is enough to sustain us a while, yeah? Listen to me going on about sustain, odd word isn't it? You two could outlast an apocalypse, survivors you are! Bet you've got errands to run, laundry to do, groceries to put away—er, I've been meaning to ask, do you still make that lovely Pasta dish that Arthur seemed to hate so much? The one covered in weird extra-long confetti?"

"String cheese, Doctor. It was a dare. And my husband does the laundry, thanks. You never quite live it down once you've turned your spouse's favorite pair of black pants to light pink. Why the rush? Itis been a few seconds since I left, right?"

He smiled, successfully evading the question. Was it possible she never took notice, or is his smile more cunning then before? That feeling came over her again; only this time it made her skin itch and the small hairs on her neck stand up like she'd stepped into some kind of electrical field. "You know, I wasn't kidding about the apocalypse, its amazing what you can do with cheese and a bit of antibacterial hair gel in the 27th century."

"Anti-what?"

"Never mind. It's an entirely alternative dimension and heavily centered on New Age technology—eventually leading to their demise. You wouldn't believe it if I showed you. Nothing really important there though— even if your kids did jump start a new race. Still. Like I said, you should be running along, you've got work tomorrow haven't you?"

"Why? Trying to get rid of me already? Rory doesn't care much, anyway." She quipped and choosing (yes choosing) to forget that little tidbit, if not just to see how much he was paying attention.

"No, I'm trying to protect you. And that's not true. Amy, you know that's not true." He turned, flicking some switches, no doubt setting the coordinates for home when she saw how serious he was.

She stood at this, thoroughly angry at having her departure planned for her and still reeling with adrenaline from the near escape they made and her prior assumptions.

"From what? A few crazed locals and some violet colored sand? We've handled worse!" She scoffed as he crossed his arms and leaned against the console. "Think you know everything, do you? Well, tough! We're not the perfect and happy couple you want us to be."

"Because you treat me like I should! I never said I wanted you to be perfect, but happy? Yes. You know, I'm afraid Rory was right, I do make people want to impress me."

"Don't flatter yourself."

Apparently she had crossed some new line by provoking him when he suddenly shoved her, he was a lot stronger than she'd first given him credit for, and she landed with a slight thud on the captain's chair, determinedly pinned underneath him.

"Get off!" She pushed against him, but his grip on her wrists above her head was firm. "Doctor, please..."

He was inches from her face and she could feel his hot breath, tinged with sweet smell of citrus and vanilla from the pie they'd eaten earlier on some long forgotten and unknown planet, 'Deva' something or other. Maybe Cronous.

His eyes narrowed mockingly, and his entire demeanor changed. It was like watching a fuse being blown. "What's wrong, Amelia? Are you scared? I thought this was what you wanted."

He had gone back to that dreadful fairytale name again and it made her teeth grind. She shook her head slowly, as if finally coming to the conclusion that she was playing with a very dangerous fire but too transfixed by the flames and almost getting burned to turn away. "No, you know that's not what I..."

"Mmm? Not what you expected, or is it more than what you are willing to see?"

She tried to buck him off, but that simply resulted in a smirk thrown in her direction and the dawning realization that despite him not being much taller than her, the weight difference is certainly a contributing factor at this present moment. "Aw, poor little Amelia can't get her way. What ever are we to do about that?"

At that tone of voice alone she could almost bring herself to hate him. He was always quick to use her faults against her, leaving the real problems left unsaid or for much later when she could barely remember what they were fighting about to begin with.

"Doctor, why are you doing this? What happened to you?"

"Nothing you couldn't fix, I'm sure."

"Stop it. Just stop!" She struggled in vain, though his hold was steady. She'd pictured several times what it would be like to have the Doctor stretched out over her, without a stitch of clothing between them, but nothing close to this. He was actually scaring her, something she wouldn't admit to anyone. Least of all letting it show to him in such a defenseless position.

He grinned, apparently enjoying his power over her. "Should I? I'm only fulfilling what you've always wanted. What we've both wanted. Isn't that what the Dream Lord said? He was right, wasn't he?"

"No! Doctor, whatever this is you've got to fight it."

"Fight? Why would I need to?" His brow furrowed. For a second she thought he looked genuinely confused until he chuckled. The low sound vibrating across her and sending more chills up her spine, not nearly as unpleasant as she would've thought. There was something about the way those grey eyes were gazing at her, almost hypnotic and possessing a strange white glow...

"Amelia, open you're eyes." He whispered in a guttural voice, snapping her out of some trance-like state and regain feeling into her limbs after being trapped under him for what felt like hours, in reality it must have been minutes.

"Stop saying that name and get a hold of yourself. You're turning into a monster!"

"Well, it's your name isn't it? Besides, you liked it. You knew what I was capable of from the beginning and on you stayed. I'm sure you remember the Starship."

How could she forget? There was no time to relive the past however, whatever had taken over the Doctor had to be stopped now.

He ran a finger through her fine red hair and down to her cheek. "I'm not a monster, I just know the difference between obviously wanting something and getting it, in oppose to denying it altogether and saving myself the trouble of waiting. Can't you see? We could—"

A slap that would've resounded off the walls was stopped in mid air when he caught her hand. Were his reflexes usually this fast? She thought as he gave her a sad look, distrust evident in his eyes.

"You shouldn't do that, Amy."

"Then get off of me or you'll never see me again." It was her turn to glare as she shoved him a bit and stood, straightening her skirt and hair. Those words seemed to have more effect on him than anything and caused his vice grip to loosen.

He blinked rapidly, trying to clear his vision. As if discovering for the first time where he was and what he'd done. "I'm...I'm sorry. Are you all right?" He swallowed hard against the lump in his throat, making his voice raspy. "Oh God, I'm so sorry."

She didn't answer. Her back to him, arms folded tightly. "You were bitten."

"What? Oh, yes.... Raingards, I believe." He adjusted his jacket and leaned on the console out of sheer support. Why did it feel like he was suddenly being choked? And those things he'd said—he barely understood half of it and what came over him, she'd never forgive him. He only hoped that she would at least forget, given time. "They were back at the Station. They are an ancient race and not easy to kill, at least not all of them at once. Maybe the Entity released more than I...They like dark and old places the most..."

Amy's hands were shaking and her palms started to sweat and she could hardly focus on what he was saying, but she kept them folded behind her. He had apologized and didn't want to make the situation worse by suggesting he scared her more than she let on, maybe whatever it was that took control earlier is gone for now and if he was willing to avoid it then so was she.

"So... are they along the lines of an alien virus or are they immortal? Like the Norse god, Thor? You said they were ancient."

Doctor looked up from the console, smiling a bit and seemingly back to his old, informative self. "Thor? You know about Mythology?"

Amy allowed herself to walk a few feet towards him, with the console conveniently placed between them.

"I may have...done some light reading for a project in school, but he's the only one I could think of." He snickered and she punched him playfully on the shoulder, still cautious of what he might do in such close proximity. "Shut up."

"That's actually a misconception. They only give the appearance of immortality because they age at a snail's pace, for lack of a better word. Also, when Asgardians eat the Golden Apples that are cultivated by the goddess Idunn, they are able to keep themselves in tip-top shape. No, Raingards are different."

"Oh." Very intelligent, nice to know he has no impact on you by any means. "Well...How?"

"That's the way it is, Amy."

She nodded. "Not telling us, then?"

"There are just...some things you aren't meant to know in depth. It's nothing to panic over. A slight change in mood, really," He paused, head down— the atmosphere had definitely changed, it was awkward and they were trying too hard to make everything that occurred normal. He knew it was a lousy explanation, but he didn't care to push that broken envelope any further. There was a war in his mind. He could beat it, but no doubt it would take a regeneration or two to actually heal, if at all. That part of him, that darkest part would never leave and something had just made it swam to the surface more than he was accustomed to dealing with.

"Take my word for it." He winked, catching the flicker of disappointment scatter across her features, perhaps wondering why he has a tendency to shut her out and treat her like a child when the discussion finally got interesting.

"Doctor, what happened? What have they done to you?"

He sighed. At times he did love her adventurous, flirty, and daring personality, but she could also be annoyingly stubborn and right now was not one of those times.

"You should leave, Amy. I'll visit you again and all of us will go somewhere with a wonderful view, promise. But you need to go."

"Not until you tell me what the hell is going on. Why are you doing this?"

He grimaced, glancing around nervously at every corner of the ship except at her.

"Because I can't control myself around you."

"What do you mean?"

"There's something in your blood, something that makes me ache, and that is certainly a good reason for you to leave."

 _She made him ache? With what, need?_  She thought that was all behind them now. She had Rory, and he had...

The TARDIS.

He was pushing her away; Amy knew he hadn't meant to say those things. Neither had she. But what else was he hiding?

"And that's it? One last trip and off you go?"

"You don't understand, I—"

"No, you don't understand! You get to leave but we stay and deal with the consequences. Are you really going to be a coward about this?"

"I'm not. I can't do it with you on board and risk your life again."

"Yes you are. What does it matter? Hasn't there been enough risk already? We've come through fine."

"You've come through without a CHOICE. I led you to believe you're..." He faltered and she could see how wet his eyes were getting.

"We're what? Go on."

"Invincible. This isn't something you can fix and expect it to instantly disappear, Amy. Neither of you can because it doesn't work. It never works."

"God, you always do this! You think we're completely fragile until for one brief moment we prove you wrong and you're praising us," She spat the words out with enough malice to make him cringe. "You know what? I don't want your praise, I never did. I want to help; I want to help because you've been there for us. For me. And I don't need your fucking logic about what humans are, you just don't get it, and you never will because you aren't human.

The Doctor was clutching a lever so hard his knuckles were white; he sucked in a deep breath and looked at her as much contempt as he could gather. If she wouldn't go willingly, he'd have to make her.

"Get out."

"No, Doctor you have to let me—"

He slammed his fist on the console, making her jump and step away from him. "AMELIA, GET. OUT. NOW!"

She wiped at her face, tears falling freely. She turned and was surprised to see the TARDIS doors already open, her backdoor standing patronizingly clear a few yards away. She saw the upstairs light on and knew Rory must've heard the TARDIS materializing. No doubt waiting for her with a cuppa and reading some novel. She stared at him for a moment longer, in a last ditch effort before walking out into the damp night to convince him that she only wants what is best for him, her raggedy man— and she should've said this, but she knows he won't listen. 

\------

The blue vase now sits condescendingly, not perfectly, in the middle of the old but sturdy dining room table. Rory says it's cheerful and livens up the house, though Amy knows better than to think for a second that this is true. She finds that after all they have gone through, regardless of the Doctor, he's still eager to please her in any little way possible, as much as she loves him for it, she can't help but feel it gnawing at her nerves and crushing remorse of how unfair it is to him when he's only trying to work through a difficult time, its real and the pain is still raw because they're in it together. Sometimes she wonders how she manages to hold in the scream that threatens to rip itself from her throat.

_A scream that says we're fine. We can overcome this and don't need to use the Doctor as an excuse anymore. We'll never be what our friends describe as 'OK' at dinner parties when they think we're out of earshot, but at least we can move on. Why can't you just be happy with that? Why did you have to put on such a fucking false face and make me look like the depressed and stupid one for holding you back? When I know you're as scarred as I am if not more._

She has a brief moment of wanting to do just that, as she watches her husband set the table for a long anticipated guest (they can't control this thing called the universe and its co-conspirator Fate, so why should they worry?), but backed out at the very last minute when he looked at her with some concern. She shook her head, smiling a little awkwardly at having been caught in deep thought.

The doorbell rings and she thanks whoever is in charge of the cosmos that she can escape the dining room.

When she opens the door, there is a smear of red on his left hand, which he noticed her staring at and silently wiped it off on his pants. She didn't ask and he was glad as they greeted him with hugs and he sat down at the table next to Rory. Brave, but delectably oblivious Rory who sometimes let things slide when he knew they couldn't be helped.

She took her seat and passed around the salad bowl.

She hadn't asked, not yet.

Because the Doctor hated endings.

**Author's Note:**

> I didn't mean the end to play out so ominously. Actually, the whole thing is pretty ominous; it all kind of just spiraled. I really didn't want to go the Vampire route, it's been done and...well, there are other options, right? Like letting the reader guess? Yeah. Sometimes I think it's not what we think or say that defies us as scary, but what's lurking in our very core. On a side note, it was complete luck that the Jade Vine happens to look sort of blue as well as being a rare flower. If the video is not working, let me know.
> 
> Thanks for reading!


End file.
